X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=2420cf7318a5feb0a6030622076bd9f1febf29f9;hb=66e2ef1a1a7767b8ca8d40f108f29e9036166236;hp=13f8d7f7a2ea43b39579fb2fc22c564b0a745dc2;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 13f8d7f..2420cf7 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,18 +21,25 @@ package jalview.appletgui; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.renderer.ScaleRenderer; +import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; import java.awt.Color; import java.awt.FontMetrics; import java.awt.Graphics; import java.awt.Image; import java.awt.Panel; +import java.beans.PropertyChangeEvent; +import java.util.List; -public class SeqCanvas extends Panel +public class SeqCanvas extends Panel implements ViewportListenerI { FeatureRenderer fr; @@ -48,8 +55,6 @@ public class SeqCanvas extends Panel AlignViewport av; - SearchResults searchResults = null; - boolean fastPaint = false; int cursorX = 0; @@ -63,6 +68,8 @@ public class SeqCanvas extends Panel sr = new SequenceRenderer(av); PaintRefresher.Register(this, av.getSequenceSetId()); updateViewport(); + + av.getRanges().addPropertyChangeListener(this); } int avcharHeight = 0, avcharWidth = 0; @@ -90,26 +97,29 @@ public class SeqCanvas extends Panel private void drawNorthScale(Graphics g, int startx, int endx, int ypos) { - int scalestartx = startx - startx % 10 + 10; - + updateViewport(); g.setColor(Color.black); - - // NORTH SCALE - for (int i = scalestartx; i < endx; i += 10) + for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx, + endx)) { - int value = i; - if (av.hasHiddenColumns()) + int mpos = mark.column; // (i - startx - 1) + if (mpos < 0) { - value = av.getColumnSelection().adjustForHiddenColumns(value); + continue; } + String mstring = mark.text; - g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth, - ypos - (avcharHeight / 2)); - - g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2), - (ypos + 2) - (avcharHeight / 2), - ((i - startx - 1) * avcharWidth) + (avcharWidth / 2), - ypos - 2); + if (mark.major) + { + if (mstring != null) + { + g.drawString(mstring, mpos * avcharWidth, + ypos - (avcharHeight / 2)); + } + g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), + (ypos + 2) - (avcharHeight / 2), + (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2); + } } } @@ -119,14 +129,17 @@ public class SeqCanvas extends Panel ypos += avcharHeight; if (av.hasHiddenColumns()) { - startx = av.getColumnSelection().adjustForHiddenColumns(startx); - endx = av.getColumnSelection().adjustForHiddenColumns(endx); + startx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(startx); + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); } int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } // WEST SCALE @@ -154,8 +167,8 @@ public class SeqCanvas extends Panel { int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) - avcharWidth / 2; - g.drawString(value + "", x, (ypos + (i * avcharHeight)) - - (avcharHeight / 5)); + g.drawString(value + "", x, + (ypos + (i * avcharHeight)) - (avcharHeight / 5)); } } } @@ -166,7 +179,8 @@ public class SeqCanvas extends Panel if (av.hasHiddenColumns()) { - endx = av.getColumnSelection().adjustForHiddenColumns(endx); + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); } SequenceI seq; @@ -193,8 +207,8 @@ public class SeqCanvas extends Panel if (value != -1) { - g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight)) - - (avcharHeight / 5)); + g.drawString(String.valueOf(value), 0, + (ypos + (i * avcharHeight)) - (avcharHeight / 5)); } } } @@ -208,25 +222,29 @@ public class SeqCanvas extends Panel return; } + ViewportRanges ranges = av.getRanges(); + updateViewport(); // Its possible on certain browsers that the call to fastpaint // is faster than it can paint, so this check here catches // this possibility - if (lastsr + horizontal != av.startRes) + if (lastsr + horizontal != ranges.getStartRes()) { - horizontal = av.startRes - lastsr; + horizontal = ranges.getStartRes() - lastsr; } - lastsr = av.startRes; + lastsr = ranges.getStartRes(); fastPaint = true; - gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth - - horizontal * avcharWidth, + gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, + imgWidth - horizontal * avcharWidth, imgHeight - vertical * avcharHeight, -horizontal * avcharWidth, -vertical * avcharHeight); - int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0; + int sr = ranges.getStartRes(), er = ranges.getEndRes(), + ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0, + transY = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { @@ -241,21 +259,23 @@ public class SeqCanvas extends Panel else if (vertical > 0) // scroll down { ss = es - vertical; - if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time + if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page + // at a + // time { - ss = av.startSeq; + ss = ranges.getStartSeq(); } else { - transY = imgHeight - vertical * avcharHeight; + transY = imgHeight - ((vertical + 1) * avcharHeight); } } else if (vertical < 0) { es = ss - vertical; - if (es > av.endSeq) + if (es > ranges.getEndSeq()) { - es = av.endSeq; + es = ranges.getEndSeq(); } } @@ -276,6 +296,7 @@ public class SeqCanvas extends Panel * at 0). NOTE 1: The av limits are set in setFont in this class and in the * adjustment listener in SeqPanel when the scrollbars move. */ + @Override public void update(Graphics g) { paint(g); @@ -286,8 +307,8 @@ public class SeqCanvas extends Panel { if (img != null - && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g - .getClipBounds().height))) + && (fastPaint || (getSize().width != g.getClipBounds().width) + || (getSize().height != g.getClipBounds().height))) { g.drawImage(img, 0, 0, this); fastPaint = false; @@ -325,13 +346,16 @@ public class SeqCanvas extends Panel gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, imgHeight); + ViewportRanges ranges = av.getRanges(); + if (av.getWrapAlignment()) { - drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); + drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes()); } else { - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); } g.drawImage(img, 0, 0, this); @@ -396,6 +420,9 @@ public class SeqCanvas extends Panel FontMetrics fm = getFontMetrics(av.getFont()); + LABEL_EAST = 0; + LABEL_WEST = 0; + if (av.getScaleRightWrapped()) { LABEL_EAST = fm.stringWidth(getMask()); @@ -417,16 +444,17 @@ public class SeqCanvas extends Panel av.setWrappedWidth(cWidth); - av.endRes = av.startRes + cWidth; + av.getRanges().setViewportStartAndWidth(startRes, cWidth); int endx; int ypos = hgap; - int maxwidth = av.getAlignment().getWidth() - 1; + int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); } while ((ypos <= canvasHeight) && (startRes < maxwidth)) @@ -460,24 +488,28 @@ public class SeqCanvas extends Panel } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); g.setColor(Color.blue); int res; - for (int i = 0; i < av.getColumnSelection().getHiddenColumns() - .size(); i++) + List positions = hidden.findHiddenRegionPositions(); + for (int pos : positions) { - res = av.getColumnSelection().findHiddenRegionPosition(i) - - startRes; + res = pos - startRes; if (res < 0 || res > endx - startRes) { continue; } - gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4, - res * avcharWidth + avcharHeight / 4, res * avcharWidth }, - new int[] { ypos - (avcharHeight / 2), - ypos - (avcharHeight / 2), - ypos - (avcharHeight / 2) + 8 }, 3); + gg.fillPolygon( + new int[] + { res * avcharWidth - avcharHeight / 4, + res * avcharWidth + avcharHeight / 4, + res * avcharWidth }, + new int[] + { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), + ypos - (avcharHeight / 2) + 8 }, + 3); } } @@ -487,7 +519,7 @@ public class SeqCanvas extends Panel g.setClip(0, 0, cWidth * avcharWidth, canvasHeight); } - drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); g.setClip(null); if (av.isShowAnnotation()) @@ -527,8 +559,8 @@ public class SeqCanvas extends Panel return annotations.adjustPanelHeight(); } - private void drawPanel(Graphics g1, int startRes, int endRes, - int startSeq, int endSeq, int offset) + private void drawPanel(Graphics g1, final int startRes, final int endRes, + final int startSeq, final int endSeq, final int offset) { if (!av.hasHiddenColumns()) @@ -537,14 +569,15 @@ public class SeqCanvas extends Panel } else { - int screenY = 0; + final int screenYMax = endRes - startRes; int blockStart = startRes; int blockEnd = endRes; if (av.hasHiddenColumns()) { - for (int[] region : av.getColumnSelection().getHiddenColumns()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + for (int[] region : hidden.getHiddenColumnsCopy()) { int hideStart = region[0]; int hideEnd = region[1]; @@ -555,28 +588,44 @@ public class SeqCanvas extends Panel continue; } - blockEnd = hideStart - 1; + /* + * draw up to just before the next hidden region, or the end of + * the visible region, whichever comes first + */ + blockEnd = Math.min(hideStart - 1, blockStart + screenYMax + - screenY); g1.translate(screenY * avcharWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - if (av.getShowHiddenMarkers()) + /* + * draw the downline of the hidden column marker (ScalePanel draws the + * triangle on top) if we reached it + */ + if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1) { g1.setColor(Color.blue); g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - - 1, (endSeq - startSeq) * avcharHeight - + offset); + 0 + offset, + (blockEnd - blockStart + 1) * avcharWidth - 1, + (endSeq - startSeq + 1) * avcharHeight + offset); } g1.translate(-screenY * avcharWidth, 0); screenY += blockEnd - blockStart + 1; blockStart = hideEnd + 1; + + if (screenY > screenYMax) + { + // already rendered last block + return; + } } } - if (screenY <= (endRes - startRes)) + if (screenY <= screenYMax) { + // remaining visible region to render blockEnd = blockStart + (endRes - startRes) - screenY; g1.translate(screenY * avcharWidth, 0); draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); @@ -599,7 +648,7 @@ public class SeqCanvas extends Panel // / First draw the sequences // /////////////////////////// - for (int i = startSeq; i < endSeq; i++) + for (int i = startSeq; i <= endSeq; i++) { nextSeq = av.getAlignment().getSequenceAt(i); @@ -613,24 +662,24 @@ public class SeqCanvas extends Panel if (av.isShowSequenceFeatures()) { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * avcharHeight)); + fr.drawSequence(g, nextSeq, startRes, endRes, + offset + ((i - startSeq) * avcharHeight), false); } // / Highlight search Results once all sequences have been drawn // //////////////////////////////////////////////////////// - if (searchResults != null) + if (av.hasSearchResults()) { - int[] visibleResults = searchResults.getResults(nextSeq, startRes, - endRes); + int[] visibleResults = av.getSearchResults().getResults(nextSeq, + startRes, endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) { sr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * avcharWidth, offset - + ((i - startSeq) * avcharHeight)); + visibleResults[r + 1], + (visibleResults[r] - startRes) * avcharWidth, + offset + ((i - startSeq) * avcharHeight)); } } } @@ -682,11 +731,12 @@ public class SeqCanvas extends Panel int bottom = -1; int alHeight = av.getAlignment().getHeight() - 1; - for (i = startSeq; i < endSeq; i++) + for (i = startSeq; i <= endSeq; i++) { sx = (group.getStartRes() - startRes) * avcharWidth; sy = offset + ((i - startSeq) * avcharHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1; + ex = (((group.getEndRes() + 1) - group.getStartRes()) + * avcharWidth) - 1; if (sx + ex < 0 || sx > imgWidth) { @@ -694,22 +744,20 @@ public class SeqCanvas extends Panel } if ((sx <= (endRes - startRes) * avcharWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) + && group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i))) { if ((bottom == -1) - && (i >= alHeight || !group.getSequences(null) - .contains( - av.getAlignment().getSequenceAt(i + 1)))) + && (i >= alHeight || !group.getSequences(null).contains( + av.getAlignment().getSequenceAt(i + 1)))) { bottom = sy + avcharHeight; } if (!inGroup) { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) + if (((top == -1) && (i == 0)) || !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i - 1))) { top = sy; } @@ -830,11 +878,79 @@ public class SeqCanvas extends Panel } } - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { - searchResults = results; - + av.setSearchResults(results); repaint(); } + @Override + public void propertyChange(PropertyChangeEvent evt) + { + String eventName = evt.getPropertyName(); + + if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + { + fastPaint = true; + repaint(); + return; + } + else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT)) + { + fastPaint = false; + repaint(); + return; + } + + if (!av.getWrapAlignment()) + { + int scrollX = 0; + if (eventName.equals(ViewportRanges.STARTRES) + || eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + // Make sure we're not trying to draw a panel + // larger than the visible window + if (eventName.equals(ViewportRanges.STARTRES)) + { + scrollX = (int) evt.getNewValue() - (int) evt.getOldValue(); + } + else + { + scrollX = ((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]; + } + ViewportRanges vpRanges = av.getRanges(); + int range = vpRanges.getEndRes() - vpRanges.getStartRes(); + if (scrollX > range) + { + scrollX = range; + } + else if (scrollX < -range) + { + scrollX = -range; + } + } + + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (eventName.equals(ViewportRanges.STARTRES)) + { + // scroll - startres and endres both change + fastPaint(scrollX, 0); + } + else if (eventName.equals(ViewportRanges.STARTSEQ)) + { + // scroll + fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (eventName.equals(ViewportRanges.STARTRESANDSEQ)) + { + fastPaint(scrollX, 0); + } + } + } + }